1. Field of the Invention
The present invention relates to novel polynucleotides derived from microorganisms belonging to actinomycetes (actinobacteria) and fragments thereof, polypeptides encoded by the polynucleotides and fragments thereof, polynucleotide arrays comprising the polynucleotides and fragments thereof, computer readable recording media in which the nucleotide sequences of the polynucleotide and fragments thereof have been recorded, and use of them as well as a method of using the polynucleotide and/or polypeptide sequence information to make comparisons.
2. Brief Description of the Background Art
Actinomycetes are used in producing various biological active substances comprising an antibiotic which is obtained from a precursor such as amino acid, nucleic acid, vitamin, saccharide, organic acid, analogues thereof and the like, and are very useful microorganisms industrially. Many mutants thereof are known.
For example, Streptomyces avermitilies is a Gram-positive bacterium identified as an avermectin-producing bacterium having parasiticidal activity and insecticidal activity, and avermectin is produced by mutants thereof. The avermectin is used as a parasiticide of livestock worldwide, and is used as an agent for treating and preventing human onchocerciasis in countries of tropical regions where the onchocerciasis is prevalent. The production of avermectin using Streptomyces avermitilis is carried out in a mutant (metabolic mutant) of which metabolic pathway and its regulation mechanism are changed. However, accumulation of basic genetic, biochemical and molecular biological data on actinomycetes is insufficient in comparison with Escherichia coli, Bacillus subtilis, and the like. Also, few findings have been obtained on mutated genes in biological active substance-producing mutants. Thus, there are various mechanisms, which are still unknown, of regulating the growth and metabolism of these microorganisms.
A chromosomal map by crossing of Streptomyces avermitilis ATCC 31267 is reported and it is known that its genome size is about 8,000 kb (Mol. Gen. Genet., 252: 255-265 (1996)). Calculating on the basis of the usual gene density of bacteria, it is presumed that about 8,000 genes are present in this genome of about 8,000 kb. However, only about several ten genes mainly concerning avermectin biosynthetic genes are known in Streptomyces avermitilis, and the nucleotide sequences of most genes have not been clarified hitherto.
In recent years, the full nucleotide sequence of the genomes of several microorganisms, such as Escherichia coli, Mycobacterium tuberculosis, yeast, and the like, have been determined (Science, 277: 1453-62 (1997); Nature, 393: 537-544 (1998); Nature, 387: 5-105 (1997)). Based on the thus determined full nucleotide sequences, assumption of gene regions and prediction of their function by comparison with the nucleotide sequences of known genes have been carried out. Thus, the functions of a great number of genes have been presumed, without genetic, biochemical or molecular biological experiments.
In recent years, moreover, techniques for monitoring expression levels of a great number of genes simultaneously or detecting mutations, using DNA chips, DNA arrays or the like in which a partial nucleic acid fragment of a gene or a partial nucleic acid fragment in genome DNA other than a gene is fixed to a solid support, have been developed. The techniques contribute to the analysis of microorganisms, such as yeasts, Mycobacterium tuberculosis, Mycobacterium bovis used in BCG vaccines, and the like (Science, 278: 680-686 (1997); Proc. Natl. Acad. Sci. USA, 96; 12833-38 (1999); Science, 284: 1520-23 (1999)).